scverse · grst · Nov 28, 2025 · Oct 30, 2025 · Oct 30, 2025 · Oct 30, 2025
diff --git a/packages/CellAnnotator/meta.yaml b/packages/CellAnnotator/meta.yaml
@@ -16,3 +16,4 @@ version: v0.1.3
 authors:
   - Marius1311
 test_command: pip install -e '.[test]' && pytest
+category: ecosystem
diff --git a/packages/CellCharter/meta.yaml b/packages/CellCharter/meta.yaml
@@ -19,3 +19,4 @@ authors:
   - marcovarrone
 test_command: |
   pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/CellMapper/meta.yaml b/packages/CellMapper/meta.yaml
@@ -15,3 +15,4 @@ version: v0.1.2
 authors:
   - Marius1311
 test_command: pip install -e '.[test]' && pytest
+category: ecosystem
diff --git a/packages/CellOracle/meta.yaml b/packages/CellOracle/meta.yaml
@@ -42,3 +42,4 @@ test_command: |
   pip install .
   # command to run tests
   pytest -v
+category: ecosystem
diff --git a/packages/CellRank/meta.yaml b/packages/CellRank/meta.yaml
@@ -23,3 +23,4 @@ authors:
   - WeilerP
 test_command: |
   pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/Cell_BLAST/meta.yaml b/packages/Cell_BLAST/meta.yaml
@@ -17,3 +17,4 @@ test_command: |
   pip install --upgrade pip flit
   flit install -s
   cd test && python test.py
+category: ecosystem
diff --git a/packages/CellphoneDB/meta.yaml b/packages/CellphoneDB/meta.yaml
@@ -31,3 +31,4 @@ authors:
   - zktuong
 test_command: |
   git clone git@github.com:ventolab/CellphoneDB.git && pip install cellphonedb && pip install pytest && cd CellphoneDB/cellphonedb/src/tests/ && python3 -m pytest method_tests.py
+category: ecosystem
diff --git a/packages/Cirrocumulus/meta.yaml b/packages/Cirrocumulus/meta.yaml
@@ -18,3 +18,4 @@ authors:
   - gouwens
 test_command: |
   SETUPTOOLS_SCM_PRETEND_VERSION=0.0.1 pip install .[test,parquet] && pytest
+category: ecosystem
diff --git a/packages/DoubletDetection/meta.yaml b/packages/DoubletDetection/meta.yaml
@@ -18,3 +18,4 @@ authors:
   - JonathanShor
   - ambrosejcarr
 test_command: pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/GPTBioInsightor/meta.yaml b/packages/GPTBioInsightor/meta.yaml
@@ -16,3 +16,4 @@ version: v0.3.0
 authors:
   - huangsh
 test_command: pip install "." && pytest
+category: ecosystem
diff --git a/packages/GRnnData/meta.yaml b/packages/GRnnData/meta.yaml
@@ -19,3 +19,4 @@ version: v1.1.4
 authors:
   - jkobject (jeremie kalfon)
 test_command: pip install . && make test
+category: ecosystem
diff --git a/packages/LazySlide/meta.yaml b/packages/LazySlide/meta.yaml
@@ -16,3 +16,4 @@ authors:
   - eabila
   - afrendeiro
 test_command: uv run task test
+category: ecosystem
diff --git a/packages/Mowgli/meta.yaml b/packages/Mowgli/meta.yaml
@@ -18,3 +18,4 @@ version: v0.2.0
 authors:
   - gjhuizing
 test_command: pip install . && pytest
+category: ecosystem
diff --git a/packages/Multivelo/meta.yaml b/packages/Multivelo/meta.yaml
@@ -17,3 +17,4 @@ authors:
   - jw156605
   - danielee0707
   - jacobrepucci
+category: ecosystem
diff --git a/packages/PEAKQC/meta.yaml b/packages/PEAKQC/meta.yaml
@@ -15,3 +15,4 @@ version: 0.1.3
 authors:
   - loosolab
 test_command: pip install . && pytest
+category: ecosystem
diff --git a/packages/PILOT/meta.yaml b/packages/PILOT/meta.yaml
@@ -48,3 +48,4 @@ test_command: |
   pip install pilotpy
   conda install pytest
   cd test && pytest test_pilot.py
+category: ecosystem
diff --git a/packages/ParTIpy/meta.yaml b/packages/ParTIpy/meta.yaml
@@ -16,3 +16,4 @@ version: v0.0.04
 authors:
   - psl-schaefer
   - leotenshii
+category: ecosystem
diff --git a/packages/PathML/meta.yaml b/packages/PathML/meta.yaml
@@ -25,3 +25,4 @@ authors:
   - Yu-AnChen
   - jzhang1031
 test_command: pip install "." && pytest
+category: ecosystem
diff --git a/packages/PyDESeq2/meta.yaml b/packages/PyDESeq2/meta.yaml
@@ -21,3 +21,4 @@ authors:
   - mandreux-owkin
 test_command: |
   pip install ."[dev]" && pytest
+category: ecosystem
diff --git a/packages/Rectangle/meta.yaml b/packages/Rectangle/meta.yaml
@@ -16,3 +16,4 @@ authors:
   - bernheder
 test_command: |
   pip install ."[dev,test]" && pytest
+category: ecosystem
diff --git a/packages/SC2Spa/meta.yaml b/packages/SC2Spa/meta.yaml
@@ -21,3 +21,4 @@ authors:
   - Linbu Liao
   - Kyoung Jae Won
 test_command: pip install "." && pytest
+category: ecosystem
diff --git a/packages/SCALEX/meta.yaml b/packages/SCALEX/meta.yaml
@@ -17,3 +17,4 @@ version: v1.0.3
 authors:
   - Lei Xiong
 test_command: pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/STMiner/meta.yaml b/packages/STMiner/meta.yaml
@@ -15,3 +15,4 @@ version: v1.1.0
 authors:
   - Peisen Sun
 test_command: pip install "." && pytest
+category: ecosystem
diff --git a/packages/SnapATAC2/meta.yaml b/packages/SnapATAC2/meta.yaml
@@ -0,0 +1,23 @@
+name: SnapATAC2
+description: |
+  SnapATAC2 is a scalable and modular pipeline for analyzing single-cell ATAC-seq data,
+  enabling efficient preprocessing, dimensionality reduction, clustering, and integration
+  with single-cell RNA-seq.
+project_home: https://github.com/scverse/SnapATAC2
+documentation_home: https://scverse.org/SnapATAC2/
+tutorials_home: https://scverse.org/SnapATAC2/tutorials/index.html
+publications:
+  - 10.1038/s41592-023-02139-9
+install:
+  pypi: snapatac2
+  conda: bioconda::snapatac2
+tags:
+  - ATAC-seq
+  - chromatin accessibility
+  - epigenomics
+license: MIT
+version: 2.5.0
+authors:
+  - kaizhang
+test_command: pip install ".[test]" && pytest
+category: core-framework
diff --git a/packages/anndata-for-R/meta.yaml b/packages/anndata-for-R/meta.yaml
@@ -11,3 +11,4 @@ license: MIT
 version: 0.7.5.5
 authors:
   - rcannood
+category: ecosystem
diff --git a/packages/anndata/meta.yaml b/packages/anndata/meta.yaml
@@ -0,0 +1,26 @@
+name: AnnData
+description: |
+  AnnData is a Python package for handling annotated data matrices in memory and on disk,
+  positioned between pandas and xarray. anndata offers a broad range of computationally
+  efficient features including, among others, sparse data support, lazy operations, and a
+  PyTorch interface.
+project_home: https://github.com/scverse/anndata
+documentation_home: https://anndata.readthedocs.io/en/latest/
+tutorials_home: https://anndata.readthedocs.io/en/latest/tutorials/index.html
+publications:
+  - 10.1101/2021.12.16.473007
+install:
+  pypi: anndata
+  conda: conda-forge::anndata
+tags:
+  - data structure
+  - annotated data
+  - sparse data
+license: BSD-3-Clause
+version: 0.12.4
+authors:
+  - falexwolf
+  - ivirshup
+  - flying-sheep
+  - gokceneraslan
+category: core-datastructure
diff --git a/packages/annsel/meta.yaml b/packages/annsel/meta.yaml
@@ -18,3 +18,4 @@ tags:
   - utilities
 test_command: |
   pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/benGRN/meta.yaml b/packages/benGRN/meta.yaml
@@ -18,3 +18,4 @@ version: v1.2.1
 authors:
   - jkobject (jeremie kalfon)
 test_command: pip install . && make test
+category: ecosystem
diff --git a/packages/bento-tools/meta.yaml b/packages/bento-tools/meta.yaml
@@ -16,3 +16,4 @@ authors:
   - ckmah
   - noor01
 test_command: pip install "." && pytest
+category: ecosystem
diff --git a/packages/biolord/meta.yaml b/packages/biolord/meta.yaml
@@ -16,3 +16,4 @@ authors:
   - zoepiran
 test_command: |
   pip install ".[dev,test]" && pytest
+category: ecosystem
diff --git a/packages/cell2location/meta.yaml b/packages/cell2location/meta.yaml
@@ -23,3 +23,4 @@ authors:
   - Alexander Aivazidis
 test_command: |
   pip install ".[dev]" && pytest
+category: ecosystem
diff --git a/packages/cellxgene/meta.yaml b/packages/cellxgene/meta.yaml
@@ -27,3 +27,4 @@ authors:
   - mweiden
 test_command: |
   pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/dandelion/meta.yaml b/packages/dandelion/meta.yaml
@@ -25,3 +25,4 @@ authors:
   - grst
 test_command: |
   pip install "." && pytest
+category: ecosystem
diff --git a/packages/decoupler/meta.yaml b/packages/decoupler/meta.yaml
@@ -0,0 +1,23 @@
+name: decoupler
+description: |
+  decoupler is a framework containing different enrichment statistical methods to extract
+  biologically driven scores from omics data within a unified framework.
+project_home: https://github.com/scverse/decoupler
+documentation_home: https://decoupler-py.readthedocs.io/en/latest/
+tutorials_home: https://decoupler-py.readthedocs.io/en/latest/notebooks/101_getting_started.html
+publications:
+  - 10.1093/bioadv/vbac016
+install:
+  pypi: decoupler
+  conda: conda-forge::decoupler-py
+tags:
+  - enrichment analysis
+  - pathway analysis
+  - gene sets
+  - functional annotation
+license: BSD-3-Clause
+version: 2.1.1
+authors:
+  - PauBadiaM
+test_command: pip install ".[test]" && pytest
+category: core-framework
diff --git a/packages/delnx/meta.yaml b/packages/delnx/meta.yaml
@@ -18,3 +18,4 @@ authors:
   - adaml9
 test_command: |
   pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/dynamo-release/meta.yaml b/packages/dynamo-release/meta.yaml
@@ -19,3 +19,4 @@ authors:
   - dummyindex
   - yaz62
 test_command: pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/epiScanpy/meta.yaml b/packages/epiScanpy/meta.yaml
@@ -24,3 +24,4 @@ authors:
   - michalk8
   - mvinyard
 test_command: pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/eschr/meta.yaml b/packages/eschr/meta.yaml
@@ -18,3 +18,4 @@ version: v1.0.1
 authors:
   - smgoggin10
 test_command: pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/favapy/meta.yaml b/packages/favapy/meta.yaml
@@ -18,3 +18,4 @@ license: MIT
 version: v0.3.9.4
 authors:
   - mikelkou
+category: ecosystem
diff --git a/packages/flowsom/meta.yaml b/packages/flowsom/meta.yaml
@@ -25,3 +25,4 @@ authors:
   - ysaeys
   - SofieVG
 test_command: pip install "." && pytest
+category: ecosystem
diff --git a/packages/gssnng/meta.yaml b/packages/gssnng/meta.yaml
@@ -21,3 +21,4 @@ authors:
   - redst4r
 test_command: |
   git clone git@github.com:IlyaLab/gssnng.git && pip install gssnng && pip install pytest && cd gssnng/ && pytest
+category: ecosystem
diff --git a/packages/hotspot/meta.yaml b/packages/hotspot/meta.yaml
@@ -17,3 +17,4 @@ authors:
   - adamgayoso
 test_command: |
   pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/infercnvpy/meta.yaml b/packages/infercnvpy/meta.yaml
@@ -13,3 +13,4 @@ authors:
   - grst
 test_command: |
   pip install ".[test]" && pytest
+category: ecosystem
diff --git a/packages/liana/meta.yaml b/packages/liana/meta.yaml
@@ -19,3 +19,4 @@ test_command: |
   pip install poetry && \
   poetry install --extras "full" && \
   poetry run pytest --disable-warnings .
+category: ecosystem
diff --git a/packages/maxspin/meta.yaml b/packages/maxspin/meta.yaml
@@ -16,3 +16,4 @@ version: v0.1.1
 authors:
   - dcjones
 test_command: pip install "." && pytest
+category: ecosystem
diff --git a/packages/moscot/meta.yaml b/packages/moscot/meta.yaml
@@ -21,3 +21,4 @@ authors:
   - Marius1311
   - zoepiran
 test_command: pip install -e '.[dev]' && pytest
+category: ecosystem
diff --git a/packages/mudata/meta.yaml b/packages/mudata/meta.yaml
@@ -0,0 +1,23 @@
+name: MuData
+description: |
+  MuData is a format for annotated multimodal datasets where each modality is represented
+  by an AnnData object. MuData's reference implementation is in Python, and the cross-language
+  functionality is achieved via HDF5-based .h5mu files with libraries in R and Julia.
+project_home: https://github.com/scverse/mudata
+documentation_home: https://mudata.readthedocs.io/en/latest/
+tutorials_home: https://mudata.readthedocs.io/en/latest/notebooks/quickstart.html
+publications:
+  - 10.1186/s13059-021-02577-8
+install:
+  pypi: mudata
+  conda: conda-forge::mudata
+tags:
+  - data structure
+  - multimodal
+  - multi-omics
+license: BSD-3-Clause
+version: 0.3.2
+authors:
+  - gtca
+  - ilia-kats
+category: core-datastructure
diff --git a/packages/muon/meta.yaml b/packages/muon/meta.yaml
@@ -0,0 +1,21 @@
+name: Muon
+description: |
+  muon is a Python framework for multimodal omics analysis. It provides functionality
+  for working with multimodal data, including preprocessing, integration, and visualization.
+project_home: https://github.com/scverse/muon
+documentation_home: https://muon.readthedocs.io/en/latest/
+tutorials_home: https://muon-tutorials.readthedocs.io/en/latest/
+publications:
+  - 10.1186/s13059-021-02577-8
+install:
+  pypi: muon
+tags:
+  - multimodal
+  - multi-omics
+  - integration
+license: BSD-3-Clause
+version: 0.1.7
+authors:
+  - gtca
+test_command: pip install ".[test]" && pytest
+category: core-framework
diff --git a/packages/novae/meta.yaml b/packages/novae/meta.yaml
@@ -18,3 +18,4 @@ version: v0.2.1
 authors:
   - quentinblampey
 test_command: pip install ".[dev]" && pytest
+category: ecosystem
diff --git a/packages/omicverse/meta.yaml b/packages/omicverse/meta.yaml
@@ -21,3 +21,4 @@ authors:
   - DBinary
   - JuliaMYQ
 test_command: pip install "." && pytest
+category: ecosystem
diff --git a/packages/palantir/meta.yaml b/packages/palantir/meta.yaml
@@ -31,3 +31,4 @@ authors:
   - dpeerlab
   - katosh
 test_command: pip install -e '.' && pip install flake8 pytest coverage typing-extensions && pytest
+category: ecosystem
diff --git a/packages/panpipes/meta.yaml b/packages/panpipes/meta.yaml
@@ -28,3 +28,4 @@ authors:
   - Zethson
   - wlason
 test_command: pip install -e '.[dev]' && pytest
+category: ecosystem
diff --git a/packages/pegasus/meta.yaml b/packages/pegasus/meta.yaml
@@ -24,3 +24,4 @@ authors:
   - slowkow
   - jlchang
 test_command: pip install "." && pytest
+category: ecosystem
diff --git a/packages/pertpy/meta.yaml b/packages/pertpy/meta.yaml
@@ -0,0 +1,22 @@
+name: Pertpy
+description: |
+  Pertpy is a framework for analyzing large-scale single-cell perturbation experiments.
+  It harmonizes datasets, automates metadata annotation, calculates perturbation distances,
+  and analyzes cellular responses to genetic modifications, drugs, and environmental changes.
+project_home: https://github.com/scverse/pertpy
+documentation_home: https://pertpy.readthedocs.io/en/stable/
+tutorials_home: https://pertpy.readthedocs.io/en/stable/tutorials/index.html
+install:
+  pypi: pertpy
+  conda: conda-forge::pertpy
+tags:
+  - perturbation
+  - drug response
+  - CRISPR
+  - genetic perturbation
+license: MIT
+version: 1.0.3
+authors:
+  - Zethson
+test_command: pip install ".[test]" && pytest
+category: core-framework
diff --git a/packages/popV/meta.yaml b/packages/popV/meta.yaml
@@ -14,3 +14,4 @@ version: v0.5.2
 authors:
   - canergen
 test_command: pip install -e '.[test]' && pytest
+category: ecosystem
diff --git a/packages/pyLemur/meta.yaml b/packages/pyLemur/meta.yaml
@@ -17,3 +17,4 @@ version: v0.1.0
 authors:
   - Constantin Ahlmann-Eltze
 test_command: pip install -e '.[dev]' && pytest
+category: ecosystem
diff --git a/packages/pySCENIC/meta.yaml b/packages/pySCENIC/meta.yaml
@@ -29,3 +29,4 @@ authors:
   - simonvh
   - loremendez
 test_command: pip install "." && pytest
+category: ecosystem
-Original file line number
+Diff line change
@@ Expand Up / @@ -16,3 +16,4 @@ authors: @@
       - ckmah
       - noor01
     test_command: pip install "." && pytest
+    category: ecosystem